Yes, that is the correct interpretation of the colors

On 12/3/2019 9:51 AM, Ferraro, Pilar wrote:
>          External Email - Use Caution
>
> Yes, absolutely, this should work! Many Thanks!
> I have just one last question concerning the colors in FreeView.
> I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) 
> after.
> The contrast matrix is 1 -1 0.
> Among the results I see blue and red regions in Freeview. Am I correct 
> assuming that blue regions are the ones where cortical thickness is reduced 
> in patients relative to HC (correcting for disease duration)?
> I just wanted to ask for a confirmation.
>
> Many thanks,
>
> Pilar
>> Message: 2
>> Date: Mon, 2 Dec 2019 16:06:54 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one
>>      variable
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <c8973136-8b3d-801a-9e88-2d6b8fd39...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> It sounds like it would be a one-group, two-variable situation, like this
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
>> Is that not correct?
>>
>>
>> On 11/28/2019 5:24 AM, Ferraro, Pilar wrote:
>>
>>         External Email - Use Caution
>>
>> Hi,
>>
>> I apologize if I did not explain my issue properly.
>> I'm interested in looking at age-related thickness reductions in 1 group 
>> (patients), but I'd like to also account for the effect of disease duration.
>> We can say that in my case disease duration is the nuisance factor.
>> Briefly, I have the same issue reported in here 
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html), 
>> but with only one group.
>> How would you recommend to proceed?
>>
>> Many  thanks,
>>
>> Pilar
>>
>> ________________________________
>> Message: 2
>> Date: Wed, 27 Nov 2019 16:56:20 +0000
>> From: "Greve, Douglas N.,Ph.D." 
>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>>         36
>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
>> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: 
>> <fbb77a97-61b5-fac5-e2b3-0ee327e29...@mgh.harvard.edu><mailto:fbb77a97-61b5-fac5-e2b3-0ee327e29...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> what is the difference between and independent variable and a covariate?
>>
>> On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
>>>          External Email - Use Caution
>>>
>>> Yes, I did.
>>> But in this case I have two factors, not only one. In particular, I have an 
>>> independent variable X and a covariate I?d like to include in the model.
>>> How would you suggest to proceed?
>>>
>>>
>>> Thanks,
>>>
>>> Pilar
>>
>>
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>> Message: 3
>> Date: Mon, 2 Dec 2019 16:08:08 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] fsfast no run directories
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <41b08316-678f-ff4e-aa09-86993b0c7...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> In the bold directory, it looks like you have one run directory called "1". 
>> Change this to "001"
>>
>> On 11/29/2019 1:48 AM, Renew Andrade wrote:
>>
>>         External Email - Use Caution
>>
>> Dear FreeSurfer experts:
>> I have some issues with "preproc-sess" because I cannot seem to get the 
>> setup of the directory structure or files to connect different things(the T1 
>> subjects with functional bold or rest files). I have this output.
>>
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess 
>> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>> --------------------------------------------------------------
>> preproc-sess logfile is log/preproc-sess.sess1.log
>> --------------------------------------------------------------
>> $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
>> root
>> setenv FREESURFER_HOME /usr/local/freesurfer
>> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>> Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 
>> 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>> /home/andraderenew/Downloads/barrios/project
>> /usr/local/freesurfer/fsfast/bin/preproc-sess
>> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>> vie nov 29 07:33:28 CET 2019
>> instem   f
>> mc   1     f fmcpr
>> stc  1    fmcpr fmcpr.up
>> sm   0
>> mask 1   brain
>> sess1 Template -----------------------------
>> mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project 
>> -fsd bold -update
>>
>> Session: /home/andraderenew/Downloads/barrios/project/sess1 ----------------
>> vie nov 29 07:33:28 CET 2019
>> ERROR: no run directories found
>>
>>
>>
>> my working directory is
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd
>> /home/andraderenew/Downloads/barrios/project
>>
>> and
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls
>> copy.sh  sess1   sess2  sess4  sess6  sess8  sessidlist
>> log      sess10  sess3  sess5  sess7  sess9  sessidlist~
>>
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls
>> bold  rest  subjectname
>>
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1#  cd 
>> bold
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls
>> 1
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# 
>> cd 1
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# 
>> ls
>> sub-0030689_task-resthypnotic_bold.nii.gz
>>
>>
>>
>> And that is all. If I try with tutorial data there is no problem. One of the 
>> obvious differences is SUBJECTS_DIR is pointing not to subjects in 
>> freesurfer but to another folder where also is fsaverage. I don't know if 
>> this is required or I am missing another linking file.
>>
>> There you can see the files I have searched with terminal.
>>
>> Sincerely,
>> Andrade.
>>
>>
>>
>> _______________________________________________
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>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 2 Dec 2019 16:10:20 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Problems about registration and tksurfer
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <edc3d070-848e-d108-7fc1-df9243447...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Try using mri_vol2surf to sample your fMRI onto the surface, then load it as 
>> a surface overlay in freeview
>>
>> On 11/29/2019 3:35 AM, ?? wrote:
>>
>>         External Email - Use Caution
>>
>> Dear madam or sir,
>>     I'm a student in China who use the Freesurfer to analyse my fMRI data 
>> and overlay some results on the surface. I met some problems about 
>> registration when I map my retinotopic results on the surface.
>>     I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and 
>> the sulutions are matrix, the rows are voxels and the column is polar angle 
>> or eccentricity. So I replaced the BOLD values by the solutions in a volume 
>> image, for example, the polar angle solution, and I used it as overlay 
>> volume image, meanwhile I used the original volume image which is same but 
>> BOLD value didn't been changed as the template image to register, but 
>> whichever methods listed in the multimodal registration I used, the overlay 
>> volume image couldn't been overlaid in correct position on the inflated 
>> surface by freeview, just like the pic1.png in the attachment, at the same 
>> time the overlay volume image could been overlaid on the orig surface in 
>> correct position like the pic2.png in the attachment, so my first problem is 
>> why the inflated surface couldn't be overlaid correctly but the orig surface 
>> could be with the same registration data and what can I do to make the 
>> overlay volume image overlay on the inflated surface in correct position by 
>> freeview?
>>    Moreover I also used tksurfer to overlay, fortunately the overlay volume 
>> image could overlay on the inflated surface in correct position. But the 
>> overlay color scale couldn't be color wheel like the red-green-blue. 
>> Furthermore, the display in the tksurfer is upside down just like the 
>> pic3.png in the attachment. So my second problem is if there are some ways 
>> to make the tksurfer color scale like the freeview and how to make the 
>> tksurfer display correctly?
>>    Best regards,
>>    Qing Zhu
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 2 Dec 2019 16:12:42 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] about mri_vol2surf and mri_surf2surf
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <d49f91cf-9b15-0645-28a7-a9a557d60...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>>
>> On 11/29/2019 4:27 AM, ??? wrote:
>>
>>         External Email - Use Caution
>>
>> Hello,
>>
>> I have some questions about the command of mri_vol2surf and mri_surf2surf
>>
>> 1. For fMRI data, I find previous paper reported that they used standard 
>> SPM8 preprocessing routines, no normalize to standard MNI152 template. The 
>> T-map images were translated to the individual cortical surface by using 
>> mri_vol2surf function, and then by using mri_sur2surf, all images were 
>> translated to the fsaverage space for intersubject comparison. But for me, I 
>> use the FsFAST to analysis our fMRI data and get each individual P-value 
>> result about sig.nii.gz. How do I use mri_surf2surf function, for 
>> translating to fsaverage space? Would I use the preprocessing with fsaverage 
>> directly?
>>
>> It might already be on fsaverage, depending upon how you did the analysis. 
>> What was your mkanalysis-sess command?
>>
>>
>> 2. For quantitative T1 and MTV data, the pervious paper reported that they 
>> used similar method (mri_vol2surf and mri_surf2surf).
>>
>> Where can I get the register.dat, when I use the mri_vol2surf function? May 
>> I understand it estimates the the relation fMRI and T1? Would I use the 
>> mri_vol2surf function and obtain an individual's surf data in fsaverage 
>> space directly?
>>
>> Use bbregister
>>
>>
>> 3. For labels, can I make a mask about the BA44 area in which structure is 
>> simile with the file sig.nii.gz? How?
>> Again, it depends on what space your sig.nii.gz is in. If it is in fsaverage 
>> space, then you don't need to do anything more
>>
>> Best wished!
>> Qianqian Yu
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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>>
>> Message: 6
>> Date: Mon, 2 Dec 2019 16:18:49 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Multiple comparison using Monte Carlo
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <c8beebe3-c9dc-6523-1b6d-dee753689...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> That will use the pre-computed ("cached") CSD files distributed with 
>> FreeSurfer. This used 10,000 iterations.
>>
>> On 12/1/2019 11:34 PM, Ting Li wrote:
>>
>>         External Email - Use Caution
>>
>> Dear Freesurfer Expert:
>>
>> I have used the simulation code as show below:
>>
>>
>> mri_glmfit-sim \
>>   --glmdir lh.gender_age.glmdir \
>>   --cache 4 neg \
>>   --cwp  0.05\
>>   --2spaces
>>
>> My question is how many iterations are done during this simulation? I didn?t 
>> specify the iteration number.
>>
>> Why I didn?t have the csd file?
>>
>> Thanks a lot for your response!
>>
>> Best regards,
>> Ting
>>
>>
>>
>> _______________________________________________
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>> ------------------------------
>>
>> Message: 7
>> Date: Mon, 2 Dec 2019 16:17:37 +0000
>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Question on GLM - correlation
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <2fb25ca2-dfd3-e49e-684a-8cf439c10...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> I'm not sure what you are doing here. You say that you have two continuous 
>> variables, but there is only one in the fsgd file. The contrast has 3 items, 
>> but it would test for the offset, not the slope. Also, why do you have 
>> --no-prune?
>>
>> On 11/29/2019 3:08 PM, Barletta, Valeria wrote:
>> Dear Freesurfers,
>> I am running glmfit to assess for correlation between y and another continue 
>> variable across the cortex (ficvf), correcting for the effect of age, using 
>> the command:
>>
>> mri_glmfit \
>>   --y {surfname_cme}.mgh \
>>   --fsgd {contrast}.fsgd \
>>   --C {contrast}.mat \
>>   --pvr ${hemi}.ficvf.mgh" \
>>   --surf fsaverage $hemi \
>>   --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \
>>   --no-prune
>>
>> This is my matrix:
>> 1 0 0
>>
>> And my fsgd file:
>>
>> Title CME
>> Class MS
>> Variable age
>> Input MS069_R01_01  MS  29
>> Input MS070_R01_02_R1year  MS  44
>> Input MS072_R01_04  MS  38
>> Input MS073_R01_05 MS 47
>> Input MS075_R01_07_R1year MS 34
>> Input MS076_R01_08 MS 25
>> Input MS077_R01_09 MS 30
>> Input MS078_R01_10 MS 22
>> Input MS080_R01_12 MS 52
>> Input MS081_R01_13 MS 31
>> Input MS082_R01_14 MS 37
>> Input MS084_R01_16 MS 42
>> Input MS086_R01_18 MS 28
>> Input MS087_R01_19_R1year MS 39
>> Input MS088_R01_20 MS 44
>> Input MS089_R01_29 MS 44
>> Input MS090_R01_21 MS 32
>> Input MS091_R01_22 MS 32
>> Input MS092_R01_23 MS 36
>> Input MS094_R01_25 MS 47
>> Input MS104_R01_36 MS 52
>>
>>
>> This is the result:
>> [cid:part1.9EE9F34D.23B9DFF4@mgh.harvard.edu][cid:part2.A1889CBE.3AAE2CA4@mgh.harvard.edu]
>>
>> Am I proceeding correctly?
>>
>> Thank you,
>> Valeria
>>
>>
>>
>>
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